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base repository: mlin/spVCF
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base: v0.0.1
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head repository: mlin/spVCF
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Commits on Jun 27, 2018
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Periodically emit a full dense row, to aid partial decoding.
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Commits on Jun 28, 2018
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Commits on Jun 30, 2018
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Revise squeezing logic to truncate cells to GT:DP if there's no evidence for any alternate allele based on AD/VR
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Commits on Jul 1, 2018
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A bunch of gnarly tricks to speed up the encoder: avoiding stringstream, reducing copying & allocation, using lookup table, etc.
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speed up decoder with homebrew ostringstream
It is absurd that in 2018 i have to write this myself to get good performance.
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Commits on Jul 2, 2018
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Commits on Jul 6, 2018
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Commits on Jul 8, 2018
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Commits on Jul 9, 2018
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Commits on Jul 10, 2018
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Commits on Jul 15, 2018
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Commits on Jul 21, 2018
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On each sparse line, convey the POS of the last full dense row (check…
…point) This added INFO field is useful for random access and partial decoding of the spVCF file.
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Subcommand 'spvcf tabix my.spvcf.gz chr21:1234-2345' can take a genomic range slice of a bgzipped, tabix-indexed spVCF file, producing spVCF that can be decoded back to pVCF standalone.
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Commits on Jul 28, 2018
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Commits on Jul 29, 2018
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Commits on Jul 31, 2018
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Commits on Aug 1, 2018
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Commits on Aug 15, 2018
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Commits on Aug 22, 2018
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squeeze: omit trailing run of missing fields even in cells that aren'…
…t lossily truncated
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Commits on Aug 23, 2018
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Commits on Aug 27, 2018
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Commits on Aug 29, 2018
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The encoder can run multithreaded by buffering batches of input lines and processing each batch in a worker thread. In favorable circumstances this yields higher throughput than the default single-threaded approach, but there is a trade-off of greatly increased memory usage and copying. Activated with -t,--threads.
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Commits on Oct 2, 2018
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Spec change: never quote-encode cells whose genotypes aren't referenc…
…e-identical or non-called This ensures all non-reference genotypes on a row can be read without reference to any previous row, a significant convenience in exchange for a negligible size increase.
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Commits on Oct 4, 2018
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Commits on Oct 14, 2018
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Commits on Oct 16, 2018
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Commits on Feb 5, 2019
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Commits on Mar 13, 2019
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change ##fileformat to and fro
Unfortunate side effect, tabix needs to be given -p vcf
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